1-244401724-C-T

Variant names:

• chr1-244401724-C-T
• rs3102475
• ENST00000417765.1:n.157+6988G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417765.1(ENSG00000240963):​n.157+6988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 151,988 control chromosomes in the GnomAD database, including 46,110 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46110 hom., cov: 31)
• Consequence: ENSG00000240963 ENST00000417765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 3 publications found

Genes affected

ENSG00000240963 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000240963	ENST00000417765.1	n.157+6988G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117831 AN: 151870 Hom.: 46057 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.761

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 117943 AN: 151988 Hom.: 46110 Cov.: 31 AF XY: 0.776 AC XY: 57651 AN XY: 74268

African (AFR) AF: 0.846 AC: 35069 AN: 41458

American (AMR) AF: 0.818 AC: 12505 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2485 AN: 3460

East Asian (EAS) AF: 0.850 AC: 4402 AN: 5178

South Asian (SAS) AF: 0.847 AC: 4076 AN: 4810

European-Finnish (FIN) AF: 0.687 AC: 7222 AN: 10512

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.728 AC: 49498 AN: 67970

Other (OTH) AF: 0.764 AC: 1613 AN: 2112

Alfa AF: 0.762 Hom.: 7040

Bravo AF: 0.790

Asia WGS AF: 0.837 AC: 2911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3102475; hg19: chr1-244565026;